2006 Toyota Matrix Problems: 4 Issues Every Owner Should Know
2006 model year · 2,780+ owner reports · Updated April 2026
According to Au7o's analysis of 2,780+ owner reports, the 2006 Toyota Matrix has 4 documented known issues. No issues are rated critical, indicating generally reliable ownership. The most commonly reported issue is Rear Hatch Strut Failure with 1,800 owner reports. Across all issues, repair costs range from $20 to $1,500. DIY maintenance guides at au7o.io.
All 4 Known Issues
On the 2003-2008 Toyota Matrix, 1st-gen Matrix models are prone to rust at the rocker panels, rear wheel arches, and rear hatch seam areas in salt-belt regions. The rust starts from inside the rocker panel and works outward, often being severe before it becomes visible on the exterior.
Common Symptoms
- Bubbling paint on rocker panels
- Rust perforation at rear wheel arches
- Visible rust at rear hatch seams
- Rocker panels soft to the touch
- Paint flaking along lower body panels
How to Fix
For early rust: sand to bare metal, treat with POR-15 or Eastwood Rust Encapsulator, prime and paint. Moderate rust: cut out affected metal and weld in patch panels. Aftermarket rocker panels available from RockAuto. For prevention, apply Fluid Film or rubberized undercoating to inner rocker panels annually. Address any paint chips immediately to prevent rust initiation.
What Owners Are Using
Parts and tips from 980+ owners who fixed this issue
- Tip
- Tip
- UpgradePOR-15 rust preventive coating stops rust permanently (POR-15 Rust Preventive Coating)
- UpgradeRust-Oleum rust converter spray for treating corroded panels (Rust-Oleum Rust Converter Spray)
- UpgradeStrongArm liftgate struts — easy bolt-on replacement (StrongArm Liftgate Support Struts)
- UpgradeSachs OE-quality liftgate gas struts (Sachs Liftgate Gas Struts)
On the 2003-2014 Toyota Matrix, the rear hatch lift support struts lose their gas charge, causing the hatch to fall or not stay open. This is a common issue on all Matrix model years, typically failing between 5-8 years of age. A falling hatch is a safety hazard.
Common Symptoms
- Rear hatch won't stay open
- Hatch falls down when released
- Hatch opens slowly or partially
- Need to prop hatch open manually
How to Fix
Replace both hatch struts (sold in pairs). Genuine Toyota 68960-02061 or aftermarket equivalents from StrongArm (6117), Sachs, or Monroe. Simple DIY replacement with a flat screwdriver to pop off the ball socket clips. Takes less than 10 minutes. Always replace both struts at the same time.
What Owners Are Using
Parts and tips from 1,800+ owners who fixed this issue
- Tip
- Tip
- UpgradeStrongArm liftgate struts — easy bolt-on replacement (StrongArm Liftgate Support Struts)
- UpgradeSachs OE-quality liftgate gas struts (Sachs Liftgate Gas Struts)
On the 2003-2008 Toyota Matrix, the first-generation Matrix (2003-2008) is notorious for water leaking into the rear cargo area through deteriorated taillight gaskets. Water pools in the spare tire well and can damage the cargo floor, cause mold/mildew, and corrode the spare tire hardware. The taillight mounting studs pass through the body panel and the factory sealant deteriorates over time.
Common Symptoms
- Water in spare tire well
- Damp or musty smell in cargo area
- Wet carpet in rear of vehicle
- Mold growth in cargo area
- Water visible after rain or car wash
How to Fix
Remove both taillights and clean the mounting surfaces. Apply a bead of black RTV silicone or butyl tape around the taillight gasket surface before reinstalling. Ensure all mounting studs are tight but not over-torqued (which cracks the taillight housing). Check and reseal the rear hatch weatherstrip if it's also deteriorated. Dry out the spare tire well completely to prevent mold.
What Owners Are Using
Parts and tips from 0+ owners who fixed this issue
- TipButyl tape from the hardware store works better than RTV for the taillight seal. It compresses and fills gaps, and won't harden and crack like silicone does over time. $5 fix.
- UpgradeDorman weatherstrip seal prevents water leaks and wind noise (Dorman Weatherstrip Seal)
- Upgrade3M Super Weatherstrip Adhesive for reattaching loose seals (3M Weatherstrip Adhesive)
On the 2003-2014 Toyota Matrix, matrix rear hatch gas struts lose pressure over time, causing the hatch to fail to stay open and drop unexpectedly. This is a common issue on both generations, typically occurring between 5-8 years of age. The failing struts create a safety hazard as the heavy hatch can strike the person loading or unloading the cargo area. Cold weather accelerates strut failure.
Common Symptoms
- Hatch won't stay open on its own
- Hatch drops when released
- Hatch opens slowly or only partially
- Worse in cold weather
How to Fix
Replace both rear hatch struts as a pair ($30-$60 for a pair of aftermarket struts). The replacement is a simple 10-minute DIY job requiring only a flathead screwdriver or small pry bar to pop the ball studs off. Use OEM Toyota struts for longest life or Sachs/StrongArm aftermarket for a budget option. Replace every 5-7 years as preventive maintenance.
What Owners Are Using
Parts and tips from 0+ owners who fixed this issue
- TipStrongArm brand struts from RockAuto are $25 for a pair and last 5+ years. One of the easiest DIY jobs on the Matrix — no tools needed, just pop off the old clips and snap on new ones.
- UpgradeStrongArm liftgate struts — easy bolt-on replacement (StrongArm Liftgate Support Struts)
- UpgradeSachs OE-quality liftgate gas struts (Sachs Liftgate Gas Struts)